Packaging research artefacts with RO-Crate

Soiland‐Reyes, Stian; Sefton, Peter; Crosas, Mercè; Castro, Leyla Jael; Coppens, Frederik; Fernández, José Marı́a; Garijo, Daniel; Grüning, Björn; Rosa, M.; Leo, Simone; Carragáin, Eoghan Ó; Portier, Marc; Trisovic, A.; Community, RO-Crate; Groth, Paul; Goble, Carole

doi:10.5281/zenodo.5146228

Cited by 4 publications

(4 citation statements)

References 3 publications

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“…Regarding the proposed standards for simulations, encourages the separation of concerns by using a fixed folder structure and README files. Moreover, aims to work towards full compatibility with the COMBINE archive standard (Bergmann et al, 2014) and RO-crate (Soiland-Reyes et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

standard-GEM: standardization of open-source genome-scale metabolic models

Anton

Almaas

Benfeitas

et al. 2023

Preprint

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The field of metabolic modelling at the genome-scale continues to grow with more models being created and curated. This comes with an increasing demand for adopting common principles regarding transparency and versioning, in addition to standardisation efforts regarding file formats, annotation and testing. Here, we present a standardised template for git-based and GitHub-hosted genome-scale metabolic models (GEMs) supporting both new models and curated ones, following FAIR principles (findability, accessibility, interoperability, and reusability), and incorporating best-practices. Standard-GEM facilitates the reuse of GEMs across web services and platforms in the metabolic modelling field and enables automatic validation of GEMs. The use of this template for new models, and its adoption for existing ones, paves the way for increasing model quality, openness, and accessibility with minimal effort.

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Section: Discussionmentioning

confidence: 99%

standard-GEM: standardization of open-source genome-scale metabolic models

Anton

Almaas

Benfeitas

et al. 2023

Preprint

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“…These are commonly used in HTML to provide metadata that is reused by search engines. schema.org schemas are also used as basis for metadata in RO-Crate [37]. Additionally, there is ongoing work 1 to add missing terms from the CodeMeta schema [22] to schema.org.…”

Section: Formatsmentioning

confidence: 99%

“…schema.org RO-Crate [37] uses schema.org [17] schemas to record and provide core metadata. Both Dataverse project and InvenioRDM offer metadata exports as schema.org JSON-LD.…”

Section: Integrationsmentioning

confidence: 99%

Software publications with rich metadata: state of the art, automated workflows and HERMES concept

Druskat¹,

Bertuch²,

Juckeland³

et al. 2022

Preprint

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To satisfy the principles of FAIR software, software sustainability and software citation, research software must be formally published. Publication repositories make this possible and provide published software versions with unique and persistent identifiers. However, software publication is still a tedious, mostly manual process.To streamline software publication, HERMES, a project funded by the Helmholtz Metadata Collaboration, develops automated workflows to publish research software with rich metadata.The tooling developed by the project utilizes continuous integration solutions to retrieve, collate, and process existing metadata in source repositories, and publish them on publication repositories, including checks against existing metadata requirements. To accompany the tooling and enable researchers to easily reuse it, the project also provides comprehensive documentation and templates for widely used CI solutions. In this paper, we outline the concept for these workflows, and describe how our solution advance the state of the art in research software publication.This work is licensed under 4.0.

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“…Therefore, these evaluation initiatives need guidance to ensure that their FAIRness assessments are (a) within the scope of the FAIR Principles and (b) consider the full breadth of valid technical options to enact the required metadata gathering and testing behaviours. Given the increasing number of Web standards compliant with FAIR Principles, such as the emergence of RO-Crates [6] as a mechanism to publish data-provider-sourced domain metadata, it is essential to ensure that "objectively compliant" resources are not judged "unfairly" due to their selection of one technology or standard versus another.…”

Section: Rationalementioning

confidence: 99%

Community-driven governance of FAIRness assessment: an open issue, an open discussion

Wilkinson¹,

Sansone²,

Méndez³

et al. 2022

Open Res Europe

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Although FAIR Research Data Principles are targeted at and implemented by different communities, research disciplines, and research stakeholders (data stewards, curators, etc.), there is no conclusive way to determine the level of FAIRness intended or required to make research artefacts (including, but not limited to, research data) Findable, Accessible, Interoperable, and Reusable. The FAIR Principles cover all types of digital objects, metadata, and infrastructures. However, they focus their narrative on data features that support their reusability. FAIR defines principles, not standards, and therefore they do not propose a mechanism to achieve the behaviours they describe in an attempt to be technology/implementation neutral. A range of FAIR assessment metrics and tools have been designed that measure FAIRness. Unfortunately, the same digital objects assessed by different tools often exhibit widely different outcomes because of these independent interpretations of FAIR. This results in confusion among the publishers, the funders, and the users of digital research objects. Moreover, in the absence of a standard and transparent definition of what constitutes FAIR behaviours, there is a temptation to define existing approaches as being FAIR-compliant rather than having FAIR define the expected behaviours. This whitepaper identifies three high-level stakeholder categories -FAIR decision and policymakers, FAIR custodians, and FAIR practitioners - and provides examples outlining specific stakeholders' (hypothetical but anticipated) needs. It also examines possible models for governance based on the existing peer efforts, standardisation bodies, and other ways to acknowledge specifications and potential benefits. This whitepaper can serve as a starting point to foster an open discussion around FAIRness governance and the mechanism(s) that could be used to implement it, to be trusted, broadly representative, appropriately scoped, and sustainable. We invite engagement in this conversation in an open Google Group fair-assessment-governance@googlegroups.com

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Packaging research artefacts with RO-Crate

Cited by 4 publications

References 3 publications

standard-GEM: standardization of open-source genome-scale metabolic models

standard-GEM: standardization of open-source genome-scale metabolic models

Software publications with rich metadata: state of the art, automated workflows and HERMES concept

Community-driven governance of FAIRness assessment: an open issue, an open discussion

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